Publications tagged "Methylation"
Oxford Nanopore and Genomics England announce new strategic research project to resolve undiagnosed rare disease cases
Oxford Nanopore sequencing technology will be used in a pioneering new collaboration with Genomics England, to sequence as many as 7,500 samples from participants of the landmark 100,000 ...
Oxford Nanopore releases new machine learning model to enable real-time, high-accuracy epigenetic insights in biological analyses
Oxford Nanopore expands capabilities for methylation analysis, giving users the ability to capture epigenetic insights in humans, animals, plants and bacteria
Oxford Nanopore at ASHG 2021: find out how you can use nanopore technology to gain comprehensive, scalable, accurate insights in human genomics
As researchers convene for ASHG online, we’re looking forward to hearing about the very latest in human genomics research using nanopore sequencing over the next few days. We've pulled to...
Methylartist: Tools for visualising modified bases from nanopore sequence data
Methylartist is a consolidated suite of tools for processing, visualising, and analysing nanopore methylation data derived from modified basecalling methods. All detectable methylation types (e.g. 5...
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes. Comprehensive analyses of large, composite or arra...
EpiNano: detection of m6A RNA modifications using Oxford Nanopore direct RNA sequencing
RNA modifications play pivotal roles in the RNA life cycle and RNA fate, and are now appreciated as a major posttranscriptional regulatory layer in the cell. In the last few years, direct RNA nanop...
The epiallelic nature of mouse rDNA
Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. Here we report that 45S rDNA units in the C57BL/6J mouse strain are epiallelic, existing as distinct ...
High-quality Arabidopsis thaliana genome assembly with Nanopore and HiFi long reads
Here, we report a high-quality (HQ) and almost complete genome assembly with a single gap and quality value (QV) larger than 60 of the model plant Arabidopsis thaliana ecotype Columbia (Col-0), gene...
Whole human genome 5'-mC methylation analysis using long read nanopore sequencing
DNA methylation is a type of epigenetic modification that affects gene expression regulation and is associated with several human diseases. Microarray and short read sequencing technologies are ofte...
DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
Background Nanopore long-read sequencing technology greatly expands the capacity of long-range single-molecule DNA-modification detection. A growing number of analytical tools have been actively dev...
MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads. Importantly, ...
Interview: The PromethION Experts at VIB
with Mojca Strazisar, Tim De Pooter and Wouter De Coster, members of the VIB Center for Molecular Neurology Conducted and written by Jonathan Pugh “Yields have been exploding in th...
NERD-seq: A novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs
The new next-generation sequencing platforms by Oxford Nanopore Technologies for direct RNA sequencing (direct RNA-seq) allow for an in-depth and comprehensive study of the epitranscriptome by enabl...
Interview: Using PromethION for Cancer, Collaborations and more
with Dr Richard Moore, Sequencing Group Leader at the Genome Science Centre, BC Cancer Conducted and written by Jonathan Pugh
Innovations with ultra-long reads
The panel session at London Calling 2021 online saw three leading researchers present their latest work using ultra-long nanopore sequencing reads, obtained using the Ultra-Long DNA Seque...
The human ribosomal RNA gene is composed of highly homogenized tandem clusters
The structure of the human ribosomal RNA gene clustering region (rDNA) has traditionally been hard to analyze due to its highly repetitive nature. However, the recent development of long-read sequen...
The genetic and epigenetic landscape of the Arabidopsis centromeres
Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used ultra-lo...
The mitochondrial genome and epigenome of the golden lion tamarin from fecal DNA using nanopore adaptive sequencing
The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this sp...
Epigenetic patterns in a complete human genome
The completion of the first telomere-to-telomere human genome, T2T-CHM13, enables exploration of the full epigenome, removing limitations previously imposed by the missing reference sequence. Existi...
A comparative analysis of computational tools for the prediction of epigenetic DNA methylation from long-read sequencing data
Recent development of Oxford Nanopore long-read sequencing has opened new avenues of identifying epigenetic DNA methylation. Among the different epigenetic DNA methylations, N6-methyladenosine is th...
Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome
Short tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG S...
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing...
Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure
Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In the majority of convent...
Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots
Epitranscriptomic modifications constitute a gene expression checkpoint in all living organisms. As nitrogen is an essential element for plant growth and development, a reasonable hypothesis is that...
Principles of mRNA targeting and regulation via the Arabidopsis m6A-binding proteins ECT2 and ECT3
Gene regulation dependent on N6-methyladenosine (m6A) in mRNA involves RNA-binding proteins that recognize m6A through a YTH domain. The Arabidopsis YTH-domain protein ECT2 is thought to influence m...
Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression
Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive natur...
Transcriptional activity and epigenetic regulation of transposable element in the symbiotic fungus Rhizophagus irregularis
Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable ...
Comparison of long read sequencing technologies in interrogating bacteria and fly genomes
The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technolo...
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data
DNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification...
Robust methylation-based classification of brain tumors using nanopore sequencing
DNA methylation-based classification of cancer provides a comprehensive molecular approach to diagnose tumors. In fact, DNA methylation profiling of human brain tumors already profoundly impacts cli...
Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T
Background There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and...
The GGC repeat expansion in NOTCH2NLC is associated with oculopharyngodistal myopathy type 3
Oculopharyngodistal myopathy (OPDM) is an adult-onset neuromuscular disease characterized by progressive ocular, facial, pharyngeal and distal limb muscle involvement. Trinucleotide repeat expansion...
Alpha satellite insertions and the evolutionary landscape of centromeres
Human centromeres are composed of alpha satellite DNA hierarchically organized as higher-order repeats and epigenetically specified by CENP-A binding. Current evolutionary models assert that new cen...
Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing
Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multi...
A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental genes partitioning in Toxoplasma
Correct 3’end processing of mRNAs is regarded as one of the regulatory cornerstones of gene expression. In a parasite that must answer to the high regulatory requirements of its multi-host life styl...
Oxford Nanopore sequencing-based protocol to detect CpG methylation in human mitochondrial DNA
Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole ge...
On the application of BERT models for nanopore methylation detection
Motivation DNA methylation is a common epigenetic modification, which is widely associated with various biological processes, such as gene expression, aging, and disease. Nanopore sequencing provide...
Genome-wide detection of cytosine methylations in plant from Nanopore sequencing data using deep learning
Methylation states of DNA bases can be detected from native Nanopore reads directly. At present, there are many computational methods that can detect 5mCs in CpG contexts accurately by Nanopore sequ...
DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing
Symbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, su...
Analysis of mitochondrial genome methylation using Nanopore single-molecule sequencing
The level and the biological significance of mitochondrial DNA (mtDNA) methylation in human cells is a controversial topic. Using long-read third-generation sequencing technology, mtDNA methylation ...
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis
Background Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioi...
DNAModAnnot: a R toolbox for DNA modification filtering and annotation
Motivation Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect th...
NanoMethViz: an R/Bioconductor package for visualizing long-read methylation data
Motivation A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. Tools for effective visualization of data generated by thi...
Comparison of long read sequencing technologies in resolving bacteria and fly genomes
Background The newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has de...
A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions
There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, littl...
Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS
We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level inp...
Short and long-read sequencing survey of the dynamic transcriptomes of African swine fever virus and its host
African swine fever virus (ASFV) is an important animal pathogen causing substantial economic losses in the swine industry globally. At present, little is known about the molecular biology of ASFV, ...
NanoReviser: an error-correction tool for Nanopore sequencing based on a deep learning algorithm
Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. Since 2014, Oxford Nanopore Technologies (ONT) has developed a series of devices based on...
Detection and discrimination of DNA adducts differing in size, regiochemistry and functional group by nanopore sequencing
Chemically induced DNA adducts can lead to mutations and cancer. Unfortunately, because common analytical methods (e.g., liquid chromatography-mass spectrometry) require adducts to be digested or li...
In vivo genetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia
An enhanced requirement for extracellular nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy for evaluating dependencies in acute myeloid leuk...
Dynamic Methylome Modification associated with mutational signatures in ageing and etiology of disease
Epigenetic markers and reversible change in the loci of genes regulating critical cell processes, have recently emerged as important biomarkers in the study of disease pathology. The epigenetic chan...
nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification
Advances in Nanopore single-molecule direct RNA sequencing (DRS) have presented the possibility of detecting comprehensive post-transcriptional modifications (PTMs) as an alternative to experimental...
Systematic benchmarking of tools for CpG methylation detection from Nanopore sequencing
DNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy ...
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complex...
Long-read assembly of the Brassica napus reference genome Darmor-bzh
Background The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a...
Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes
Hepatitis B virus (HBV) contains a 3.2 kb DNA genome and causes acute and chronic hepatitis. HBV infection is a global health problem, with 350 million chronically infected people at increased risk ...
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predict...
Minimal detection and low biological fluctuation of mitochondrial CpG methylation at the single-molecule level
Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is...
The structure, function, and evolution of a complete human chromosome 8
The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembl...
New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs
Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current ‘RNA-sequencing’ technologies produce a relatively short...
Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing
A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular re...
New Twists in Detecting mRNA Modification Dynamics
Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucle...
Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts
Motivation Nucleotides modification status can be decoded from the Oxford Nanopore Technologies (ONT) nanopore sequencing ionic current signals. Although various algorithms have been developed for n...
A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma
Molecular biomarkers provide both diagnostic and prognostic results for patients with diffuse glioma, the most common primary brain tumor in adults. Here, we used a long-read nanopore-based sequen...
Detection of differential RNA modifications from direct RNA sequencing of human cell lines
Differences in RNA expression can provide insights into the molecular identity of a cell, pathways involved in human diseases, and variation in RNA levels across patients associated with clinical ph...
Direct detection of RNA modifications and structure using single molecule nanopore sequencing
Many methods exist to detect RNA modifications by short-read sequencing, relying on either antibody enrichment of transcripts bearing modified bases or mutational profiling approaches which require ...
Nanopore sequencing enables comprehensive transposable element epigenomic profiling
Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape o...
The architecture of SARS-CoV-2 transcriptome
SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complemen...
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing
Nanopore sequencing provides a great opportunity for direct detection of chemical DNA modification. However, existing computational methods were either trained for detecting a specific form of DNA m...
Nanopore sequencing in blood diseases: a wide range of opportunities
The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disor...
Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5′ or 3′ splice site or polyad...
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type...
High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome
High-quality nanopore genome assemblies were generated for two Brassica nigra genotypes (Ni100 and CN115125); a member of the agronomically important Brassica species. The N50 contig length for th...
Profiling of human gut virome with Oxford Nanopore technology
The human gut virome plays critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology. Yet, there are insufficient amount of studies on this...
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUnt...
Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications
The prokaryotic transcriptome is shaped by transcriptional and posttranscriptional events that define the characteristics of an RNA, including transcript boundaries, the base modification status, an...
Nanopore sequencing of native adeno-associated virus single-stranded DNA using a transposase-based rapid protocol
Monitoring DNA integrity and DNA contaminants in adeno-associated virus (AAV) gene therapy vectors is of major interest, because of clinical applications with increasing therapeutic doses. We here ...
Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution
The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cyto...
Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-met...
RNA modifications detection by comparative Nanopore direct RNA sequencing
Abstract RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. To date, over 150 naturally occurring P...
Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing
Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-ba...
MasterOfPores: A workflow for the analysis of Oxford Nanopore Direct RNA sequencing datasets
The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplif...
Recent advances in the detection of base modifications using the nanopore sequencer
DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in...
Combinatorial analysis of Saccharomyces cerevisiae regulatory elements
Gene expression in Saccharomyces cerevisiae is regulated at multiple levels. Genomic and epigenomic mapping of transcription factors and chromatin components has led to the definition and delineatio...
Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type ...
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequenc...
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Background Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de no...
Targeted nanopore sequencing with Cas9-guided adapter ligation
Despite recent improvements in sequencing methods, there remains a need for assays that provide high sequencing depth and comprehensive variant detection. Current methods are limited by the loss of ...
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
The DNA base modification N6-methyladenine (m6A) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method...
Single-molecule long-read sequencing reveals the chromatin basis of gene expression
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remains poorly studied at the single-cell level. Here we present a ...
Long-range single-molecule mapping of chromatin accessibility in eukaryotes
Active regulatory elements in eukaryotes are typically characterized by an open, nucleosome depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used too...
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromati...
Decoding the epitranscriptional landscape from native RNA sequences
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This appr...
Repeat expansion and methylation state analysis with nanopore sequencing
Expansions of short tandem repeats are genetic variants that have been implicated in neuropsychiatric and other disorders but their assessment remains challenging with current molecular methods. Her...
Using long-read sequencing to detect imprinted DNA methylation
Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylati...
Nanopore detection of bacterial DNA base modifications
The common bacterial base modification N6-methyladenine (m6A) is involved in many pathways related to an organism's ability to survive and interact with its environment. Recent research has shown th...
Detecting DNA cytosine methylation using nanopore sequencing
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanop...